MRI is central to presurgical workup for malformations of cortical development (MCD) but findings are ambiguous on morphological imaging. For example, assessments on cortical thickness may disagree with histology. We investigated whether this gap may be bridged by diffusion MRI (dMRI) with the novel ‘tensor-valued diffusion encoding’ technique. Results from thirteen patients showed WM-like content with high microscopic anisotropy within lesions that were uniform and GM-like in T1- and T2-weighted images and on conventional dMRI. As a marker of axonal content less confounded by myelination and orientation dispersion, tensor-valued diffusion encoding may improve MCD characterization and evaluation of cortical thickness.